The nucleus maintains the integrity of genes and to controls the activities of the cell by regulating gene expression.
The structure of the nucleus is comprised of:
The Nucleolus
The Nuclear Envelope
Nuclear Pores
Nuclear Lamina
The Nucleolus:
The nucleolus is not bound by a membrane, and mainly synthesizes ribosomal RNA and assembles ribosomes.
The size of this sub-nuclear structure depend upon the ribosomal requirements of its cell. Cells that produce large amounts of proteins have larger nucleoli, sometimes taking up as much as one-fourth of the nucleus. The nucleolus is comprised of granular and fibrillar parts, as well as DNA. The granular parts consist of ribosomal subunits that have already been formed but have not yet matured. The fibrillar parts are mostly comprised of rRNA molecules and associated proteins that have formed fibrils.
The Nuclear Envelope:
The envelope has two layers and separates the nuclear material from the surrounding cytoplasm. The outer layer of the membrane is continuous with the rough endoplasmic reticulum, featuring numerous ribosomes studding its surface. The outer and inner layer are fused together at the nuclear pores that perforate the nuclear envelope. The space between the outer and inner layers is the perinuclear space.
Nuclear Pores: Nuclear pores regulate the passage of molecules between the nucleus and cytoplasm. The pores are permeable to small molecules down to the size of the smallest proteins. However, they form a barrier keeping out most large molecules. Some larger proteins, though, such as histones, are allowed in despite the pores appearing too small to do so. A protein structure called the nuclear pore complex is thought to be key in allowing the transport of large molecules. Pore density tends to be greatest among cells that are extremely active and differentiated, like liver cells. A normal mammalian cell features approximately 3,000 to 4,000 pores.
Nuclear Lamina: The nuclear lamina provides structural support to the nuclear envelope, specifically the inner layer.
It is a mesh-like lining which bindsto chromatin and other nuclear components. The nuclear lamina is also thought help direct materials toward the pores for export, and in the disintegration of the nuclear envelope during cell division and its later reformation. Lamins are fibrous proteins that provide structural function to the nucleus. They are also involved in the positioning of nuclear pores.
Transcription
Transcription = DNA → RNA
Translation = RNA → protein
DNA serves as the template for the synthesis of RNA.
The steps of transcription are comprised of:
50 different protein transcription factors bind to promoter sites.
An enzyme, an RNA polymerase, binds to these transcription factors.
They "unzip" the DNA double helix.
The RNA polymerase proceeds to "read" one strand. (3′ → 5′ direction)
The RNA polymerase travels along the DNA strand, it assembles ribonucleotides into a strand of RNA.
Each ribonucleotide is placed into the growing RNA strand.
For each C on the DNA strand, a G is inserted in the RNA; for G, a C; for T, an A.
However, A on the DNA calls for the insertion of the pyrimidine uracil, U.
7. Synthesis of the RNA proceeds in the 5′ → 3′ direction.
8. When transcription is complete, the transcript is released from the polymerase and, shortly thereafter, the polymerase is released from the DNA.
Kinds of RNA
Several types of RNA are synthesized:
Messenger RNA (mRNA): translated into a polypeptide.
Ribosomal RNA (rRNA): used in the building of ribosomes.
Transfer RNA (tRNA): RNA molecules that carry amino acids to the polypeptide.
Small nuclear RNA (snRNA): DNA transcription can produce large precursor molecules, primary transcripts, that must be processed to produce the functional molecules for export to the cytosol. Some of these processing steps are mediated by snRNAs.
Small nucleolar RNA (snoRNA)
Small Nuclear RNA ()
The snRNAs have various roles in the processing of the other classes of RNA. Several snRNAs are part of the spliceosomes that help convert pre-mRNA into mRNA by excising the introns and splicing the exons.
RNA Processing
All the primary transcripts produced in the nucleus must undergo processing steps to produce functional RNA molecules for export to the cytosol.
Most eukaryotic genes are split into segments.
The open reading frame (DNA sequence beginning with ATG and read in triplets until it ends with a STOP codon; an ORF is able to encode a polypeptide) of a gene contains periodic stretches of DNA calling for amino acids that do not occur in the actual protein product. These get transcribed into RNA but not translated into protein and are called introns. Stretches of DNA that do code for amino acids in the protein are called exons.
Introns tend to be much longer than exons.
Removal of introns — and the subsequent splicing of exons together — are essential among the steps in synthesizing mRNA.
The steps of RNA processing:
Synthesis of the cap. This is a modified guanine (G) which is attached to the 5′ end of the pre-mRNA as it emerges from RNA polymerase. The cap
protects the RNA from being degraded by enzymes that degrade RNA from the 5′ end
2. Removal of introns in the pre-mRNA and
splicing of the exons. This takes place as the
pre-mRNA continues to emerge from the RNA polymerase.
3. Synthesis of the poly(A) tail. This is a stretch of adenine (A)
nucleotides, and the transcript is cut there, and
the poly(A) tail is attached to the exposed 3′ end. This completes
the mRNA molecule.
Spliceosomes
The removal of introns and splicing of exons is done by spliceosomes, complexes of 5 snRNA moleculesand 145 different proteinssubunits.
This process is referred to as splicing.
The introns in most pre-mRNAs begin with a GU and end with an AG. These smal sequences possibly assist in guiding the spliceosome.
Research
Author: Katharine S. Ullman
Title:
Versatility at the nuclear pore complex: lessons learned from the nucleoporin Nup153
Abstract: Nup153 is one of about 30 proteins that comprise the nuclear pore complex (NPC). These proteins (termed nucleoporins or Nups) form an eight-fold symmetrical structure, with each protein present in copies of at least 8 or multiples thereof, ultimately creating a macromolecular assembly of approximately 60 MDa in vertebrates. The NPC provides a selective channel for transport of protein and ribonucleoprotein between the cytoplasm and nucleus. Nup153 is located on the nuclear face of the NPC and has roles in trafficking as well as in creating certain architectural features of the nuclear pore. Additional roles for Nup153 have emerged more recently, such as facilitating the process of nuclear disassembly at mitosis. Other nucleoporins studied to date have distinct functions but often share certain properties with Nup153. Overall, the building blocks of the nuclear pore are multifunctional, modular proteins.
-contains most of the cells genetic material
-control the activity in the cell that involves the genes
Nucleolus
-Synthesizes ribosomal RNA and constructs the ribosomes -Composed of granular and fibrillar
Nucleoplasm
-Highly viscous liquid
-nucleotides and enzymes are dissolved in it
-contains the Nuclear matrix
Nuclear Matrix- network of fibers in the Nucleoplasm
Nuclear Envelope
- Two membranes
- Outer membrane is continuous with the endoplasmic reticulum
- Ribosomes cover the surface of the outer membrane
Nuclear Pores
- Allow molecules to move through the Nuclear Envelope
-
RNA Processing
- Base pairs (introns) are subtracted from coding sequences (exons) of a gene in order to transcribe DNA into messanger RNA.
Transcription (DNA->RNA)
-The synthesis of RNA
1.Initiation- Binding of RNA polymerase to double-stranded DNA, This step involves a transition to single strandedness in the region of binding. RNA polymerase binds at a sequence of DNA called the promoter.
2.Elongation- The covalent addition of nucleotides to the three end of the growing polynucleotide chain. This involves the development of a short strech of DNA that is transiently single-stranded
3. Termination- The recognition of the transcription termination sequence and the release of RNA polymerase.
RNA Splicing
- Most of the DNA in the nucleus is made up of introns which is not needed for RNA
- The DNA is first transcribed in to a complementary RNA copy called (nuclear RNA)
- Then the introns in the nRNA is removed turning the nRNA into mRNA (messanger RNA
Spliceosomes
- Are used for splicing out the introns when creating mRNA
-Made up of five snRNA molecules and one hundred and forty five different protien subunits
Research
J. scott Butler - University of Rochester Medical Center
The biogenesis of mature eukaryotic RNAs requires post-transcriptional processing reactions that provide targets for the regulation of gene expression. Little is known about how RNA processing pathways are co-regulated to produce balanced levels of mature RNAs in response to changes in the cell's intracellular and extra-cellular environment. The research in my laboratory focuses on the roles of nuclear proteins implicated in the post-transcriptional regulation of mRNA and rRNA levels in S. cerevisiae. We are specifically interested in a recently identified complex of nucleases, called the exosome, which plays a critical role in the 3' end processing and degradation of nuclear RNAs.
Cell Nucleus
The nucleus maintains the integrity of genes and to controls the activities of the cell by regulating gene expression.
The structure of the nucleus is comprised of:
The Nucleolus:
The nucleolus is not bound by a membrane, and mainly synthesizes ribosomal RNA and assembles ribosomes.
The size of this sub-nuclear structure depend upon the ribosomal requirements of its cell. Cells that produce large amounts of proteins have larger nucleoli, sometimes taking up as much as one-fourth of the nucleus.
The nucleolus is comprised of granular and fibrillar parts, as well as DNA. The granular parts consist of ribosomal subunits that have already been formed but have not yet matured. The fibrillar parts are mostly comprised of rRNA molecules and associated proteins that have formed fibrils.
The Nuclear Envelope:
The envelope has two layers and separates the nuclear material from the surrounding cytoplasm.
The outer layer of the membrane is continuous with the rough endoplasmic reticulum, featuring numerous ribosomes studding its surface. The outer and inner layer are fused together at the nuclear pores that perforate the nuclear envelope. The space between the outer and inner layers is the perinuclear space.
Nuclear Pores:
Nuclear pores regulate the passage of molecules between the nucleus and cytoplasm.
The pores are permeable to small molecules down to the size of the smallest proteins. However, they form a barrier keeping out most large molecules. Some larger proteins, though, such as histones, are allowed in despite the pores appearing too small to do so. A protein structure called the nuclear pore complex is thought to be key in allowing the transport of large molecules.
Pore density tends to be greatest among cells that are extremely active and differe ntiated, like liver cells. A normal mammalian cell features approximately 3,000 to 4,000 pores.
Nuclear Lamina:
The nuclear lamina provides structural support to the nuclear envelope, specifically the inner layer.
It is a mesh-like lining which binds to chromatin and other nuclear components. The nuclear lamina is also thought help direct materials toward the pores for export, and in the disintegration of the nuclear envelope during cell division and its later reformation.
Lamins are fibrous proteins that provide structural function to the nucleus. They are also involved in the positioning of nu clear pores.
Transcription
- Transcription = DNA → RNA
- Translation = RNA → protein
DNA serves as the template for the synthesis of RNA.The steps of transcription are comprised of:
- For each C on the DNA strand, a G is inserted in the RNA; for G, a C; for T, an A.
- However, A on the DNA calls for the insertion of the pyrimidine uracil, U.
7. Synthesis of the RNA proceeds in the 5′ → 3′ direction.8. When transcription is complete, the transcript is released from the polymerase and, shortly thereafter, the polymerase is released from the DNA.
Kinds of RNA
Several types of RNA are synthesized:Small Nuclear RNA ()
The snRNAs have various roles in the processing of the other classes of RNA. Several snRNAs are part of the spliceosomes that help convert pre-mRNA into mRNA by excising the introns and splicing the exons.RNA Processing
All the primary transcripts produced in the nucleus must undergo processing steps to produce functional RNA molecules for export to the cytosol.
Most eukaryotic genes are split into segments.
The open reading frame (DNA sequence beginning with ATG and read in triplets until it ends with a STOP codon; an ORF is able to encode a polypeptide) of a gene contains periodic stretches of DNA calling for amino acids that do not occur in the actual protein product. These get transcribed into RNA but not translated into protein and are called introns. Stretches of DNA that do code for amino acids in the protein are called exons.
Introns tend to be much longer than exons.
Removal of introns — and the subsequent splicing of exons together — are essential among the steps in synthesizing mRNA.
The steps of RNA processing:
- protects the RNA from being degraded by enzymes that degrade RNA from the 5′ end
2. Removal of introns in the pre-mRNA andsplicing of the exons. This takes place as the
pre-mRNA continues to emerge from the RNA polymerase.
3. Synthesis of the poly(A) tail. This is a stretch of adenine (A)
nucleotides, and the transcript is cut there, and
the poly(A) tail is attached to the exposed 3′ end. This completes
the mRNA molecule.
Spliceosomes
The removal of introns and splicing of exons is done by spliceosomes, complexes of 5 snRNA molecules and 145 different proteins subunits.This process is referred to as splicing.
The introns in most pre-mRNAs begin with a GU and end with an AG. These smal sequences possibly assist in guiding the spliceosome.
Research
Author:Katharine S. Ullman
Title:
Versatility at the nuclear pore complex: lessons learned from the nucleoporin Nup153
Abstract:
Nup153 is one of about 30 proteins that comprise the nuclear pore complex (NPC). These proteins (termed nucleoporins or Nups) form an eight-fold symmetrical structure, with each protein present in copies of at least 8 or multiples thereof, ultimately creating a macromolecular assembly of approximately 60 MDa in vertebrates. The NPC provides a selective channel for transport of protein and ribonucleoprotein between the cytoplasm and nucleus. Nup153 is located on the nuclear face of the NPC and has roles in trafficking as well as in creating certain architectural features of the nuclear pore. Additional roles for Nup153 have emerged more recently, such as facilitating the process of nuclear disassembly at mitosis. Other nucleoporins studied to date have distinct functions but often share certain properties with Nup153. Overall, the building blocks of the nuclear pore are multifunctional, modular proteins.
Works Cited
“Cell Nucleus.” Wikipedia, the Free Encyclopedia. 21 Oct. 2008. Wikimedia Foundation. 21 Oct. 2008
<http://fwcdscience.wikispaces.com/Cell+Nucleus>.
Grigorieff, Nikolaus. Nikolaus Grigorieff, Brandeis University Biology Faculty Member. 8 Jan. 2007. 21 Oct. 2008
<http://www.bio.brandeis.edu/faculty/grigorieff.html>.
Kimball, John W. Biology. 6th ed. Dubuque: Wm. C. Brown, 1994. 16 Oct. 2008. 21 Oct. 2008
<http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/>.
Optical Microscopy. Dept. home page. 5 June 2008. Florida State University. 21 Oct. 2008
<http://micro.magnet.fsu.edu/>.
Parasitology Department. Dept. home page. 28 Sept. 2008. Tarbiat Modares University. 20 Oct. 2008
<http://www.modares.ac.ir/>.
The Scripps Research Institute. Dept. home page. 20 Oct. 2008. Scripps College. 21 Oct. 2008
<http://www.scripps.edu/newsandviews/e_20081020/>.
Ullman, Katherine S. Versatility at the nuclear pore complex: lessons learned from the nucleoporin
Nup153. Ullman Lab. 8 July 2008. Huntsman Cancer Institute. 21 Oct. 2008
<http://www.signaling-gateway.org/molecule/query?afcsid=A003702>.
The Cell Nucleus
Processes
-contains most of the cells genetic material-control the activity in the cell that involves the genes
Nucleolus
-Synthesizes ribosomal RNA and constructs the ribosomes-Composed of granular and fibrillar
Nucleoplasm
-Highly viscous liquid-nucleotides and enzymes are dissolved in it
-contains the Nuclear matrix
Nuclear Matrix- network of fibers in the Nucleoplasm
Nuclear Envelope
- Two membranes- Outer membrane is continuous with the endoplasmic reticulum
- Ribosomes cover the surface of the outer membrane
Nuclear Pores
- Allow molecules to move through the Nuclear Envelope-
RNA Processing
- Base pairs (introns) are subtracted from coding sequences (exons) of a gene in order to transcribe DNA into messanger RNA.
Transcription (DNA->RNA)
-The synthesis of RNA
1.Initiation- Binding of RNA polymerase to double-stranded DNA, This step involves a transition to single strandedness in the region of binding. RNA polymerase binds at a sequence of DNA called the promoter.
2.Elongation- The covalent addition of nucleotides to the three end of the growing polynucleotide chain. This involves the development of a short strech of DNA that is transiently single-stranded
3. Termination- The recognition of the transcription termination sequence and the release of RNA polymerase.
RNA Splicing
- Most of the DNA in the nucleus is made up of introns which is not needed for RNA- The DNA is first transcribed in to a complementary RNA copy called (nuclear RNA)
- Then the introns in the nRNA is removed turning the nRNA into mRNA (messanger RNA
Spliceosomes
- Are used for splicing out the introns when creating mRNA-Made up of five snRNA molecules and one hundred and forty five different protien subunits
Research
J. scott Butler - University of Rochester Medical CenterThe biogenesis of mature eukaryotic RNAs requires post-transcriptional processing reactions that provide targets for the regulation of gene expression. Little is known about how RNA processing pathways are co-regulated to produce balanced levels of mature RNAs in response to changes in the cell's intracellular and extra-cellular environment. The research in my laboratory focuses on the roles of nuclear proteins implicated in the post-transcriptional regulation of mRNA and rRNA levels in S. cerevisiae. We are specifically interested in a recently identified complex of nucleases, called the exosome, which plays a critical role in the 3' end processing and degradation of nuclear RNAs.
Bibliography
Spurger, Linda. "Cell Biology Graduate Program". University of Texas Medical Branch. 10/24/2008 <http://cellbio.utmb.edu/CELLBIO/nuclear_envelope.htm>.McClean, Phillip. "Transcription". 10/24/2008 <http://www.cc.ndsu.nodak.edu/instruct/mcclean/plsc731/transcript/transcript1.htm>
"Research Area:". University of Rochester Medical Center. 10/24/2008 <http://dbb.urmc.rochester.edu/bcbp/research_areas/ra_rna_processing.htm>.
"RNA Synthesis and Processing". National Health Museum. 10/24/2008 <http://www.accessexcellence.org/RC/VL/GG/rna_synth.php>.